Selective labeling: identifying representative sub-volumes for interactive segmentation

Automatic segmentation of challenging biomedical volumes with multiple objects is still an open research field. Automatic approaches usually require a large amount of training data to be able to model the complex and often noisy appearance and structure of biological organelles and their boundaries. However, due to the variety of different biological specimens and the large volume sizes of the datasets, training data is costly to produce, error prone and sparsely available. Here, we propose a novel Selective Labeling algorithm to overcome these challenges; an unsupervised sub-volume proposal method that identifies the most representative regions of a volume. This massively-reduced subset of regions are then manually labeled and combined with an active learning procedure to fully segment the volume. Results on a publicly available EM dataset demonstrate the quality of our approach by achieving equivalent segmentation accuracy with only 5 % of the training data

Decreasing time consumption of microscopy image segmentation through parallel processing on the GPU

The computational performance of graphical processing units (GPUs) has improved significantly. Achieving speedup factors of more than 50x compared to single-threaded CPU execution are not uncommon due to parallel processing. This makes their use for high throughput microscopy image analysis very appealing. Unfortunately, GPU programming is not straightforward and requires a lot of programming skills and effort. Additionally, the attainable speedup factor is hard to predict, since it depends on the type of algorithm, input data and the way in which the algorithm is implemented. In this paper, we identify the characteristic algorithm and data-dependent properties that significantly relate to the achievable GPU speedup. We find that the overall GPU speedup depends on three major factors: (1) the coarse-grained parallelism of the algorithm, (2) the size of the data and (3) the computation/memory transfer ratio. This is illustrated on two types of well-known segmentation methods that are extensively used in microscopy image analysis: SLIC superpixels and high-level geometric active contours. In particular, we find that our used geometric active contour segmentation algorithm is very suitable for parallel processing, resulting in acceleration factors of 50x for 0.1 megapixel images and 100x for 10 megapixel images

Electrographic changes accompanying recurrent seizures under ketogenic diet treatment.

The ketogenic diet (KD) is increasingly used to treat epilepsy refractory to antiepileptic drugs and other neurological disorders. In animal models, the KD was found to increase the threshold to seizures induced by different convulsive stimulations. However, in models in which suprathreshold stimuli were used, a paradoxical seizure worsening was consistently observed in KD-fed animals. To better define this phenomenon, we characterized the electrographic response to seizures induced in mice which were treated with the KD, and then corneally stimulated at 6-Hz in four different sessions. We also evaluated the electroencephalogram (EEG) in three patients in which the KD was associated with a paradoxical worsening of epileptic seizures. Although seizures were initially less severe, a remarkable prolongation of the electrographic response was observed in mice receiving the KD from the second session of 6-Hz corneal stimulation and onwards. The EEG was also markedly altered in the presence of progressive seizure aggravation observed in children treated with the KD, specifically one affected by Lennox\u2013Gastaut syndrome and two by type I lissencephaly. These results suggest that when seizures are induced or recur because of resistance to therapeutic interventions, the KD may change the EEG by potentiating the electrographic epileptic activity

Rapid and sensitive detection of mycobacterium ulcerans by use of a loop-mediated isothermal amplification test

This work reports the design and evaluation of a rapid loop-mediated isothermal amplification test for detecting Mycobacterium ulcerans DNA based on the multicopy insertion sequence IS2404. The test is robust and specific with a detection limit equivalent to 20 copies of the target sequence (0.01 to 0.1 genome). The test has potential for the diagnosis of Buruli ulcer under field conditions

Size Matters: Microservices Research and Applications

In this chapter we offer an overview of microservices providing the introductory information that a reader should know before continuing reading this book. We introduce the idea of microservices and we discuss some of the current research challenges and real-life software applications where the microservice paradigm play a key role. We have identified a set of areas where both researcher and developer can propose new ideas and technical solutions.Comment: arXiv admin note: text overlap with arXiv:1706.0735

Paraneoplastic Raynaud's phenomenon associated to astrocytoma

Raynaud’s phenomenon (RP) is a type of vascular disease characterized by vasoconstriction of the cutaneous arterioles in response to provoking factors such as exposure to cold temperature or emotional stress. It can be categorized as either primary or secondary. In patients affected by primary RP, the majority of cases, no underlying disease can be detected. Conversely, secondary RP is associated with a disease, most commonly connective tissue disorders such as systemic sclerosis and systemic lupus erythematosus. Further causes include drugs, occupational diseases and endocrine disorders [1—3]. Malignancy is a rarely reported cause of secondary RP. Paraneoplastic RP has been described in patients affected by malignancy. In this report, we describe a 25-year-old woman with RP attacks that occurred before diagnosis of astrocytoma and disappeared after surgical resection of the brain mass

Antiepileptogenic effects of trilostane in the kainic acid model of temporal lobe epilepsy

Objective: Epileptogenesis after status epilepticus (SE) has a faster onset in rats treated to reduce brain levels of the anticonvulsant neurosteroid allopregnanolone with the 5α-reductase inhibitor finasteride; however, it still has to be evaluated whether treatments aimed at increasing allopregnanolone levels could result in the opposite effect of delaying epileptogenesis. This possibility could be tested using the peripherally active inhibitor of 3β-hydroxysteroid dehydrogenase/Δ5-4 isomerase trilostane, which has been shown repeatedly to increase allopregnanolone levels in the brain. Methods: Trilostane (50 mg/kg) was administered subcutaneously once daily for up to six consecutive days, starting 10 min after intraperitoneal administration of kainic acid (15 mg/kg). Seizures were evaluated by video-electrocorticographic recordings for 70 days maximum, and endogenous neurosteroid levels were assessed by liquid chromatography–electrospray tandem mass spectrometry. Immunohistochemical staining was performed to evaluate the presence of brain lesions. Results: Trilostane did not alter the latency of kainic acid-induced SE onset or its overall duration. When compared to the vehicle-treated group, rats receiving six daily trilostane injections presented a remarkable delay of the first spontaneous electrocorticographic seizure and subsequent tonic–clonic spontaneous recurrent seizures (SRSs). Conversely, rats treated with only the first trilostane injection during SE did not differ from vehicle-treated rats in developing the SRSs. Notably, trilostane did not modify neuronal cell densities or the overall damage in the hippocampus. In comparison to the vehicle group, repeated administration of trilostane significantly decreased the activated microglia morphology in the subiculum. As expected, allopregnanolone and other neurosteroid levels were remarkably increased in the hippocampus and neocortex of rats treated for 6 days with trilostane, but pregnanolone was barely detectable. Neurosteroids returned to basal levels after a week of trilostane washout.. Significance: Overall, these results suggest that trilostane led to a remarkable increase in allopregnanolone brain levels, which was associated with protracted effects on epileptogenesis

The European grape berry moth, Eupoecilia ambiguella (Lepidoptera: Tortricidae): Current knowledge and management challenges

The European grape berry moth, Eupoecilia ambiguella (Hübner) (Lepidoptera: Tortricidae), since its first identification in 1796, was defined as a key pest for European viticulture despite its polyphagy. Although between the late 1800s and early 1900s its presence and spread in Europe was of concern, to date its populations are low and limited to cooler and wetter areas, leading to a decline in its importance. In the present work, we reviewed its global distribution as well as its morphology, biology, and ecology. Considering the monitoring and management of this pest, the present review summarised insecticidal, agronomic, and cultural control strategies. Moreover, given the need to reduce the impact of agriculture on the environment, humans, and non-target species, we focused on control strategies relying on pheromones and biological control agents (e.g. predators and parasitoids) involved in conservation biological control

Paleo-methane emissions recorded in foraminifera near the landward limit of the gas hydrate stability zone offshore western Svalbard

We present stable isotope and geochemical data from four sediment cores from west of Prins Karls Forland (ca. 340 m water depth), offshore western Svalbard, recovered from close to sites of active methane seepage, as well as from shallower water depths where methane seepage is not presently observed. Our analyses provide insight into the record of methane seepage in an area where ongoing ocean warming may be fueling the destabilization of shallow methane hydrate. The ?13C values of benthic and planktonic foraminifera at the methane seep sites show distinct intervals with negative values (as low as ?27.8‰) that do not coincide with the present-day depth of the sulfate methane transition zone (SMTZ). These intervals are interpreted to record long-term fluctuations in methane release at the present-day landward limit of the gas hydrate stability zone (GHSZ). Shifts in the radiocarbon ages obtained from planktonic foraminifera toward older values are related to methane-derived authigenic carbonate overgrowths of the foraminiferal tests, and prevent us from establishing the chronology of seepage events. At shallower water depths, where seepage is not presently observed, no record of past methane seepage is recorded in foraminifera from sediments spanning the last 14 ka cal BP (14C-AMS dating). ?13C values of foraminiferal carbonate tests appear to be much more sensitive to methane seepage than other sediment parameters. By providing nucleation sites for authigenic carbonate precipitation, foraminifera thus record the position of even a transiently stable SMTZ, which is likely to be a characteristic of temporally variable methane fluxes